“At least nine soldiers were beheaded... in addition to two civilians” at the checkpoint about 500 km (300 miles) south of Tripoli, Col. Ahmad Al-Mesmari said, blaming Daesh for the gruesome attack.
No group has yet claimed the dawn attack in the Al-Jufra region.
Libya has been rocked by chaos since the 2011 fall and killing of long-time dictator Muammar Qaddafi in a NATO-backed revolution.
Extremists, arms dealers and human traffickers have gained a foothold there as multiple authorities and dozens of militias vie for power.
Forces allied with the UN-backed Government of National Accord (GNA) drove Daesh militants from their stronghold of Sirte on the Mediterranean coast in December.
The head of the GNA underlined that the battle against Islamist rebels was not over, and Daesh has claimed very few attacks in Libya since.
Armed groups are continuing to hunt down members of the group who fled Sirte as the city fell. But analysts and military sources say the group remains active in Libya, particularly the desert south, where the GNA holds little sway.
Haftar, who backs a rival administration that refuses to recognize the GNA, controls much of the country’s vast southern desert.
His self-proclaimed Libyan National Army in May seized the Tamenhant base near the southern city of Sebha after driving out a pro-GNA militia.
The following month, they seized Al-Jufra, including a key military air base, from the Benghazi Defense Brigades, a coalition that includes Islamists driven out of Libya’s second city by pro-Haftar forces.
That placed the strongman in control of all the major cities and military bases in southern Libya.
Also in July, Haftar announced the “total liberation” of Benghazi, three years after he launched a military operation to seize the city.
But clashes have continued in the city, a bastion of the 2011 uprising that later fell to militants. Forces loyal to Haftar regularly blame attacks against them on Daesh, particularly in Benghazi.